def createOutput(self):
"""
Generate output html file from the path containing chemkin and dictionary files.
"""
import rmgpy.tools.generate_reactions as generate_reactions
inputFile = self.input
output_directory = self.getDirname()
generate_reactions.execute(inputFile, output_directory)
def createOutput(self):
"""
Generate output html file from the path containing chemkin and dictionary files.
"""
import rmgpy.tools.generate_reactions as generate_reactions
from rmgpy.rmg.main import initializeLog, RMG
from rmgpy.chemkin import ChemkinWriter
from rmgpy.rmg.output import OutputHTMLWriter
inputFile = self.input
output_directory = self.getDirname()
rmg = RMG()
# Add output listeners:
rmg.attach(ChemkinWriter(output_directory))
rmg.attach(OutputHTMLWriter(output_directory))
generate_reactions.execute(rmg, inputFile, output_directory)
def createOutput(self):
"""
Generate output html file from the path containing chemkin and dictionary files.
"""
import rmgpy.tools.generate_reactions as generate_reactions
from rmgpy.rmg.main import initializeLog, RMG
from rmgpy.chemkin import ChemkinWriter
from rmgpy.rmg.output import OutputHTMLWriter
inputFile = self.input
output_directory = self.getDirname()
rmg = RMG()
# Add output listeners:
rmg.attach(ChemkinWriter(output_directory))
rmg.attach(OutputHTMLWriter(output_directory))
generate_reactions.execute(rmg, inputFile, output_directory)
def test(self):
folder = os.path.join(os.path.dirname(rmgpy.__file__),
'tools/data/generate')
input_file = os.path.join(folder, 'input.py')
rmg = RMG(input_file=input_file, output_directory=folder)
rmg = execute(rmg)
self.assertIsNotNone(rmg)
self.assertIsNotNone(rmg.reaction_model.output_species_list)
self.assertIsNotNone(rmg.reaction_model.output_reaction_list)
shutil.rmtree(os.path.join(folder, 'pdep'))
def test_library_reaction_enters_core(self):
"""
Test that a reaction from a Reaction Library enters the core
right after the initialization step if all the input species are
present in that reaction.
The following reaction from the Methylformate library
HCjO + CH2O <=> Fmoml
should appear in the model if HCjO, CH2O and Fmoml are all used as input species
"""
from rmgpy.reaction import Reaction
from rmgpy.molecule import Molecule
folder = os.path.join(os.path.dirname(rmgpy.__file__),
'tools/data/generate/libraryReaction')
input_file = os.path.join(folder, 'input.py')
rmg = RMG(input_file=input_file, output_directory=folder)
rmg = execute(rmg)
self.assertIsNotNone(rmg)
# Assert that the flagged reaction occurs
rxn_flagged = Reaction(
reactants=[Molecule(smiles='[CH]=O'),
Molecule(smiles='C=O')],
products=[Molecule(smiles='[CH2]OC=O')])
count = 0
for reaction in rmg.reaction_model.core.reactions:
if reaction.is_isomorphic(rxn_flagged):
count += 1
self.assertEquals(count, 1)
# Assert that the core only has 1 reaction
self.assertEquals(len(rmg.reaction_model.core.reactions), 1)
shutil.rmtree(os.path.join(folder, 'pdep'))
def test_duplicate_reaction(self):
"""
Test that the radical addition reaction
HCJ=O + CH2O = [CH2]OC=O
present in the reaction library "Methylformate",
only appears once in the model.
"""
from rmgpy.reaction import Reaction
from rmgpy.molecule import Molecule
folder = os.path.join(os.path.dirname(rmgpy.__file__),
'tools/data/generate/duplicates')
input_file = os.path.join(folder, 'input.py')
rmg = RMG(input_file=input_file, output_directory=folder)
rmg = execute(rmg)
self.assertIsNotNone(rmg)
rxn_flagged = Reaction(
reactants=[Molecule(smiles='[CH]=O'),
Molecule(smiles='C=O')],
products=[Molecule(smiles='[CH2]OC=O')])
count = 0
for reaction in rmg.reaction_model.core.reactions:
if reaction.is_isomorphic(rxn_flagged):
count += 1
self.assertEquals(count, 1)
shutil.rmtree(os.path.join(folder, 'pdep'))